Re: [AMBER] cpin error

From: Arjun Sharma <arjunsharma83.gmail.com>
Date: Fri, 28 Aug 2015 09:00:23 -0500

I recompiled AmberTools on Ubuntu 14.04. Now it lists my residue. But I get this error when I try to run the script

cpinutil.py -p test_sol.top -igb 2 -o new.cpin -op new.top -resnames PTN
Traceback (most recent call last):
  File "/opt/amber14/bin/cpinutil.py", line 289, in <module>
    main(opt)
  File "/opt/amber14/bin/cpinutil.py", line 256, in main
    changeradii(parm, 'mbondi2').execute()
NameError: global name 'changeradii' is not defined

I donít see why it canít access the ParmedActions.py. Attached is my cpinutil.py, titratable_residues and ParmedActions.py files.

Thanks

> 6. Re: Cpin error (Arjun Sharma)
> 7. Re: Cpin error (Jason Swails)
>
>

> ------------------------------
>
> Message: 7
> Date: Thu, 27 Aug 2015 12:16:14 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Cpin error
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAEk9e3pUGkoUgSr0AUSNE9n+YrwMfeAgr-JTLgggve4+d+PGpQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Aug 27, 2015 at 11:31 AM, Arjun Sharma <arjunsharma83.gmail.com>
> wrote:
>
>> Thank you Jason for the reply. I added the new residue to to
>> titratable_residues.py but "cpinutil.py - - describe" still does not list
>> it as titratable residue at the end. Is it the atom naming or the atom
>> order in the residue that's causing the problem Why is not recognizing it
>> as a residue ?
>>
>
> ?Did you recompile AmberTools?
>

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Received on Fri Aug 28 2015 - 07:30:02 PDT
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